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Conserved domains on  [gi|106734103|gb|ABF82538|]
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DNA-directed RNA polymerase III, partial [Exiguobacterium sp. India Orange]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 1000195)

DNA-directed RNA polymerase subunit beta catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

CATH:  3.90.1110.10
EC:  2.7.7.6
Gene Ontology:  GO:0000428|GO:0003899|GO:0006351
PubMed:  6266829
SCOP:  4003708

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
2-342 0e+00

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 758.48  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEvsgDLDRYKLQKYVRSNQGTCYN 81
Cdd:PRK00405  609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGED---GVDIYNLIKFQRSNQNTCIN 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:PRK00405  686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241
Cdd:PRK00405  766 PEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEG 845

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  242 IILDVKVFDR-ENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPS 320
Cdd:PRK00405  846 TVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPS 925

                         330       340
                  ....*....|....*....|..
gi 106734103  321 RMNIGQVLELHLGMAAKKLGIK 342
Cdd:PRK00405  926 RMNIGQILETHLGWAAKGLGIK 947
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 2-342 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 758.48  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEvsgDLDRYKLQKYVRSNQGTCYN 81
Cdd:PRK00405  609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGED---GVDIYNLIKFQRSNQNTCIN 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:PRK00405  686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241
Cdd:PRK00405  766 PEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEG 845

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  242 IILDVKVFDR-ENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPS 320
Cdd:PRK00405  846 TVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPS 925

                         330       340
                  ....*....|....*....|..
gi 106734103  321 RMNIGQVLELHLGMAAKKLGIK 342
Cdd:PRK00405  926 RMNIGQILETHLGWAAKGLGIK 947
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 2-342 0e+00

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 662.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103     2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEvsGDLDRYKLQKYVRSNQGTCYN 81
Cdd:TIGR02013  566 QAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPD--GGIDIYRLLKYQRSNQDTCIN 643

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:TIGR02013  644 QRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG 723

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241
Cdd:TIGR02013  724 PEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEG 803

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   242 IILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSR 321
Cdd:TIGR02013  804 TVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883

                          330       340
                   ....*....|....*....|.
gi 106734103   322 MNIGQVLELHLGMAAKKLGIK 342
Cdd:TIGR02013  884 MNIGQILETHLGWAGKRLGRK 904
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 63-342 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 620.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   63 LDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDV 142
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  143 YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFG 222
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  223 EKAREVRDTSLRVPNGGDGIILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPY 302
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 106734103  303 MPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLGIK 342
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRR 838
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 31-342 9.45e-142

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 405.76  E-value: 9.45e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   31 VAKHPGVVERVTAREILIRRtsdvngSEVSGDLDRYKLQKYVRSNQGT---CYNQKPIIAAGdRVEKGeiladgpsmDMG 107
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQC------AMGKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAG---------GFG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  108 ELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESesRDTKLGP-EEITRDIPNVGDDALRNLDDRGII 186
Cdd:pfam00562  65 ELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEA--RKTKLGPiEEITRDIPNVSEEALKKLDEDGIV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  187 RIGAEVKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPNGGDGIILDVKVFDrengdeLSPGVNQMVR 266
Cdd:pfam00562 143 RVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVK 210

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 106734103  267 VYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLGIK 342
Cdd:pfam00562 211 VYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVF 286
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 79-342 1.53e-117

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 359.57  E-value: 1.53e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  79 CYNQKPIIaaGDRVEKgeiladgpSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDT 158
Cdd:cd00653  454 LYPQKPLV--GTGIEE--------YIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKT 523

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103 159 KLGPEEITR-DIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPN 237
Cdd:cd00653  524 KNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPG 596

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103 238 GGDGIILDVKVFDREngdeLSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLG 317
Cdd:cd00653  597 GEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHG 672

                        250       260
                 ....*....|....*....|....*
gi 106734103 318 VPSRMNIGQVLELHLGMAAKKLGIK 342
Cdd:cd00653  673 FPSRMTIGQLLESLLGKAGALLGKF 697
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 2-342 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 758.48  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEvsgDLDRYKLQKYVRSNQGTCYN 81
Cdd:PRK00405  609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGED---GVDIYNLIKFQRSNQNTCIN 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:PRK00405  686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241
Cdd:PRK00405  766 PEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEG 845

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  242 IILDVKVFDR-ENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPS 320
Cdd:PRK00405  846 TVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPS 925

                         330       340
                  ....*....|....*....|..
gi 106734103  321 RMNIGQVLELHLGMAAKKLGIK 342
Cdd:PRK00405  926 RMNIGQILETHLGWAAKGLGIK 947
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 2-342 0e+00

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 662.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103     2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEvsGDLDRYKLQKYVRSNQGTCYN 81
Cdd:TIGR02013  566 QAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPD--GGIDIYRLLKYQRSNQDTCIN 643

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:TIGR02013  644 QRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG 723

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241
Cdd:TIGR02013  724 PEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEG 803

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   242 IILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSR 321
Cdd:TIGR02013  804 TVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883

                          330       340
                   ....*....|....*....|.
gi 106734103   322 MNIGQVLELHLGMAAKKLGIK 342
Cdd:TIGR02013  884 MNIGQILETHLGWAGKRLGRK 904
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 63-342 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 620.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   63 LDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDV 142
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  143 YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFG 222
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  223 EKAREVRDTSLRVPNGGDGIILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPY 302
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 106734103  303 MPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLGIK 342
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRR 838
rpoB CHL00001
RNA polymerase beta subunit
 2-340 3.22e-157

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 467.84  E-value: 3.22e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRrtsdvngseVSGDLDRYKLQKYVRSNQGTCYN 81
Cdd:CHL00001  551 QAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILS---------GNGDTLSIPLVMYQRSNKNTCMH 621

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:CHL00001  622 QKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQG 701

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTEL--TAEERLLHAIFGEKAREVRDTSLRVPNGG 239
Cdd:CHL00001  702 PERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESsyAPEGRLLRAIFGIQVSTSKETCLKLPIGG 781

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  240 DGIILDVKVFDRENGDELSPGvnqMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVP 319
Cdd:CHL00001  782 RGRVIDVRWIQKKGGSSYNPE---TIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVP 858

                         330       340
                  ....*....|....*....|.
gi 106734103  320 SRMNIGQVLELHLGMAAKKLG 340
Cdd:CHL00001  859 SRMNVGQIFECLLGLAGDLLN 879
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-339 2.33e-156

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 465.72  E-value: 2.33e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    1 SQAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRrtsDVNGSEVSgdldrYKLQKYVRSNQGTCY 80
Cdd:CHL00207  544 RQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ---DDNNRYIH-----YYLQKYQRSNQNTCI 615

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   81 NQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKL 160
Cdd:CHL00207  616 NYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKL 695

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  161 GPEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGD 240
Cdd:CHL00207  696 GSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGY 775

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  241 GIILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPS 320
Cdd:CHL00207  776 GRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPS 855

                         330
                  ....*....|....*....
gi 106734103  321 RMNIGQVLELHLGMAAKKL 339
Cdd:CHL00207  856 RMNVGQLFECLLGLAGDNL 874
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 31-342 9.45e-142

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 405.76  E-value: 9.45e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   31 VAKHPGVVERVTAREILIRRtsdvngSEVSGDLDRYKLQKYVRSNQGT---CYNQKPIIAAGdRVEKGeiladgpsmDMG 107
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQC------AMGKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAG---------GFG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  108 ELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESesRDTKLGP-EEITRDIPNVGDDALRNLDDRGII 186
Cdd:pfam00562  65 ELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEA--RKTKLGPiEEITRDIPNVSEEALKKLDEDGIV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  187 RIGAEVKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPNGGDGIILDVKVFDrengdeLSPGVNQMVR 266
Cdd:pfam00562 143 RVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVK 210

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 106734103  267 VYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLGIK 342
Cdd:pfam00562 211 VYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVF 286
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
2-340 3.56e-124

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 393.13  E-value: 3.56e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDvNGSEVsgdlDRYKLQKYVRSNQGTCYN 81
Cdd:PRK09603  702 QAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGK-EEAYI----DAYSLQKNLRTNQNTSFN 776

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:PRK09603  777 QVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHG 856

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241
Cdd:PRK09603  857 VEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEG 936

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  242 IILDVKVF---------------------------DR------------------------------------------- 251
Cdd:PRK09603  937 TVIDVKVFtkkgyekdarvlsayeeekakldmehfDRltmlnreellrvssllsqaileepfshngkdykegdqipkeei 1016

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  252 ------------------------------------------------ENGDELSPGVNQMVRVYIVQKRKIHEGDKMAG 283
Cdd:PRK09603 1017 asinrftlaslvkkyskevqnhyeitknnfleqkkvlgeeheeklsilEKDDILPNGVIKKVKLYIATKRKLKVGDKMAG 1096

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 106734103  284 RHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLG 340
Cdd:PRK09603 1097 RHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFG 1153
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 79-342 1.53e-117

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 359.57  E-value: 1.53e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  79 CYNQKPIIaaGDRVEKgeiladgpSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDT 158
Cdd:cd00653  454 LYPQKPLV--GTGIEE--------YIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKT 523

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103 159 KLGPEEITR-DIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPN 237
Cdd:cd00653  524 KNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPG 596

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103 238 GGDGIILDVKVFDREngdeLSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLG 317
Cdd:cd00653  597 GEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHG 672

                        250       260
                 ....*....|....*....|....*
gi 106734103 318 VPSRMNIGQVLELHLGMAAKKLGIK 342
Cdd:cd00653  673 FPSRMTIGQLLESLLGKAGALLGKF 697
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
2-342 2.45e-108

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 347.38  E-value: 2.45e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103    2 QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVsgDLDRYKLQKYVRSNQGTCYN 81
Cdd:PRK14844  709 QAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYL--DVDIYHLRKFQRSNHNTCIN 786

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103   82 QKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLG 161
Cdd:PRK14844  787 QKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLG 866

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  162 PEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241
Cdd:PRK14844  867 SEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEG 946

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  242 IILDVKVF---------------------------------------------------DREN----------------- 253
Cdd:PRK14844  947 TVIDVQVFtrrgveenerallikqkeindfekerdyiinvtseyfydelkkllinsgsqDREKfdsiereqwwgiglknq 1026

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  254 ---------------------------------GDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDM 300
Cdd:PRK14844 1027 siseqvkslkkdfdekvshaiaqfkrkveklheGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDM 1106

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 106734103  301 PYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLGIK 342
Cdd:PRK14844 1107 PYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEK 1148
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 112-336 3.01e-43

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 157.50  E-value: 3.01e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  112 GRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPE-EITRDIPNV----GDDALRNLDDRGII 186
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIV 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  187 RIGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKAREVRDTSLRVPNGGDGIILDVKVFDRENGdelspgvNQM 264
Cdd:TIGR03670 278 YPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEG-------NKL 341

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 106734103  265 VRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAA 336
Cdd:TIGR03670 342 VKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVA 413
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 112-340 9.22e-42

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 153.19  E-value: 9.22e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103 112 GRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPE-EITRDIPNV----GDDALRNLDDRGII 186
Cdd:PRK07225 204 GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEdRFEIPDKDVrgyrGEEAYRHLDEDGLV 283

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103 187 RIGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKAREVRDTSLRVPNGGDGIILDVKVFDRENGdelspgvNQM 264
Cdd:PRK07225 284 NPETEVKEGDVLIGKTSPP---------RFLeePDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEG-------SRL 347

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 106734103 265 VRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLElhlgMAAKKLG 340
Cdd:PRK07225 348 VKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLE----MIGGKVG 419
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 112-336 1.10e-41

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 155.11  E-value: 1.10e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  112 GRNVVVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPE-EITRDIPNV----GDDALRNLDDRGII 186
Cdd:PRK08565  702 GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIV 781

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734103  187 RIGAEVKDGDILVGKVTPKGVTELTAEERLlhaifGEKARevRDTSLRVPNGGDGIILDVKVFDRENGdelspgvNQMVR 266
Cdd:PRK08565  782 SPEVEVKGGDVLIGKTSPPRFLEELEELSL-----GLQER--RDTSVTVRHGEKGIVDTVLITESPEG-------NKLVK 847

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 106734103  267 VYiVQKRKIHE-GDKMAGRHGNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAA 336
Cdd:PRK08565  848 VR-VRDLRIPElGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVA 917
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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